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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

0.3.1 - 2024-12-16

Compare with 0.3.1

Features

  • struct unique variant split variants by chromosome (ae7eb65 by Pierre Marijon).
  • struct genotype polars threads parameter have an effect (6419e02 by Pierre Marijon).
  • use new functionality of variantplaner_rs in variantplaner cli (f986213 by Pierre Marijon).
  • variantplaner_rs partitions could be parameterize (8b2066e by Pierre Marijon).

Bug Fixes

  • use number of bit ask by user in partitions (4409d8c by Pierre Marijon).
  • readd documentation generation (6467ee2 by Pierre Marijon).
  • transmission generation not failled if ped file contain only one line (58ee926 by Pierre Marijon).

0.3.0 - 2024-09-30

Compare with 0.2.4

Features

  • move ped code from io to object (b6638ca by Pierre Marijon).
  • parquet2vcf can extract only variant of one chromosome (f29c6ac by Pierre Marijon).
  • improve alt '*' management (755a5fa by Pierre Marijon).
  • partition support append mode (1b6603f by Pierre Marijon).
  • variant merge support append (d12d357 by Pierre Marijon).
  • Add python 3.12 in ci test and support (c51c932 by Pierre Marijon).
  • Better variant hash we only need store ref length (8a3db5e by Pierre Marijon).
  • add documentation on how interogate genotype variants partitions (b843bca by Pierre Marijon).
  • New cli (c2cb033 by Pierre Marijon).

Bug Fixes

  • add output file in struct operation only if it's exist (9a868ad by Pierre Marijon).
  • not failled if SVTYPE or SVLEN column isn't present (32a8dad by Pierre Marijon).
  • correct benchmark script run (8ebdca0 by Pierre Marijon).

Code Refactoring

  • Move many variant operation in object. (df36fa0 by Pierre Marijon).

0.2.4 - 2023-12-21

Compare with 0.2.4

Features

  • add variantplaner logo.
  • add method to compute partition value of id.

Bug Fixes

  • fix: #41 vcf spec indicate Integer must be store in 32bits.
  • update to polars 0.20.

0.2.3 - 2023-11-21

Compare with 0.2.2

Features:

  • Use ruff format in place of black
  • Minimal polars version is 0.19.15
  • SV cannot have small variant id
  • Type of id is include in part of id (all long variant are store in same place)

Fix:

  • Usage intgerate chromosome2length option

0.2.2 - 2023-10-19

Compare with first 0.2.0

Fix:

  • Correct typo in readme
  • Correct change in variantplaner_rs/Cargo.lock

0.2.1 - 2023-10-09

Compare with first 0.2.0

Fix:

  • Hot fix some lazy trouble

0.2.0 - 2023-10-02

Compare with first 0.1.0

Features:

  • Replace hash variant id by a uniq variant id
  • Improve variant transmission system to support genome with ploidie lower than 92
  • Genotype partitioning now use position part of unique id to get more local request

Fixes:

  • Documentation fix
  • Test coverage improvement

0.1.0 - 2023-07-25

Compare with first commit